[Biojava-dev] [Bug 2617] New: Cookbook blast parser example fails on a tblastn example

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2617

           Summary: Cookbook blast parser example fails on a tblastn example
           Product: BioJava
           Version: live (CVS source)
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: search
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: holland at ebi.ac.uk


(raised on behalf of user Charles Imbusch)

Hello,

for a project I want to parse a tblastn result with BioJava. I used the code
on http://biojava.org/wiki/BioJava:CookBook:Blast:Parser as it is and I get an
error message as follows:

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String
index out of range: -3
  at java.lang.String.substring(String.java:1938)
  at java.lang.String.substring(String.java:1905)
  at
org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.parseLine(BlastLikeAlignmentSAXParser.java:289)
  at
org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.parse(BlastLikeAlignmentSAXParser.java:115)
  at
org.biojava.bio.program.sax.HitSectionSAXParser.outputHSPInfo(HitSectionSAXParser.java:514)
  at
org.biojava.bio.program.sax.HitSectionSAXParser.firstHSPEvent(HitSectionSAXParser.java:287)
  at
org.biojava.bio.program.sax.HitSectionSAXParser.interpret(HitSectionSAXParser.java:251)
  at
org.biojava.bio.program.sax.HitSectionSAXParser.parse(HitSectionSAXParser.java:118)
  at
org.biojava.bio.program.sax.BlastSAXParser.hitsSectionReached(BlastSAXParser.java:635)
  at
org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java:337)
  at org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:164)
  at
org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:313)
  at
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:276)
  at
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:162)
  at BlastEcho.echo(BlastEcho.java:29)
  at BlastEcho.main(BlastEcho.java:75)

I uploaded the Blast output file I want to parse here:
http://charles.imbusch.net/tmp/blastresult.txt

Any answer is appreciated.

Cheers,
 Charles


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